Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  HUMAN ADENOSINE DEAMINASE ACTING ON DSRNA (ADAR2) MUTANT E488Q BOUND TO DSRNA SEQUENCE DERIVED FROM HUMAN GLI1 GENE
 
Authors :  M. M. Matthews, A. J. Fisher
Date :  20 Oct 15  (Deposition) - 13 Apr 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.95
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Deaminase, Human, Hydrolase-Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. M. Matthews, J. M. Thomas, Y. Zheng, K. Tran, K. J. Phelps, A. I. Scott J. Havel, A. J. Fisher, P. A. Beal
Structures Of Human Adar2 Bound To Dsrna Reveal Base-Flipping Mechanism And Basis For Site Selectivity.
Nat. Struct. Mol. Biol. V. 23 426 2016
PubMed-ID: 27065196  |  Reference-DOI: 10.1038/NSMB.3203

(-) Compounds

Molecule 1 - DOUBLE-STRANDED RNA-SPECIFIC EDITASE 1
    Chains: A, D
    EC Number: 3.5.4.37
    Engineered: YES
    Expression System: SACCHAROMYCES CEREVISIAE
    Expression System Common: YEAST
    Expression System Plasmid: PSC
    Expression System Strain: BCY123
    Expression System Taxid: 4932
    Expression System Vector Type: PLASMID
    Fragment: A TO I EDITASE (UNP RESIDUES 327-729)
    Gene: ADAR2, DRADA2, RED1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ADENOSINE DEAMINASE ACTING ON RNA
 
Molecule 2 - RNA (5'-R(P*GP*CP*UP*CP*GP*CP*GP*AP*UP*GP*CP*UP*(8AZ) P*GP*AP*GP*GP*GP*CP*UP*CP*UP*G)-3')
    Chains: B, E
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - RNA (5'- R(P*CP*AP*GP*AP*GP*CP*CP*CP*CP*CP*CP*AP*GP*CP*AP*UP*CP*GP*CP*GP*AP*GP *C)-3')
    Chains: C, F
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
18AZ2Mod. Nucleotide8-AZA-NEBULARINE-5'-MONOPHOSPHATE
2IHP2Ligand/IonINOSITOL HEXAKISPHOSPHATE
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
18AZ1Mod. Nucleotide8-AZA-NEBULARINE-5'-MONOPHOSPHATE
2IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
18AZ1Mod. Nucleotide8-AZA-NEBULARINE-5'-MONOPHOSPHATE
2IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
3ZN-1Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:391 , ILE A:397 , ARG A:400 , ARG A:401 , THR A:513 , LYS A:519 , ARG A:522 , GLY A:530 , SER A:531 , LYS A:629 , TYR A:658 , LYS A:662 , TYR A:668 , LYS A:672 , GLU A:689 , LYS A:690 , ASP A:695binding site for residue IHP A 801
2AC2SOFTWAREHIS A:394 , GLU A:396 , CYS A:451 , CYS A:516 , 8AZ B:13binding site for residue ZN A 802
3AC3SOFTWAREASN D:391 , ILE D:397 , ARG D:400 , ARG D:401 , THR D:513 , LYS D:519 , ARG D:522 , GLY D:530 , SER D:531 , LYS D:629 , TYR D:658 , LYS D:662 , TYR D:668 , LYS D:672 , TRP D:687 , GLU D:689 , LYS D:690 , ASP D:695binding site for residue IHP D 801
4AC4SOFTWAREHIS D:394 , CYS D:451 , CYS D:516 , 8AZ E:13binding site for residue ZN D 802
5AC5SOFTWAREGLY D:374 , THR D:375 , LYS D:376 , HIS D:394 , GLU D:396 , PRO D:450 , CYS D:451 , ARG D:455 , SER D:486 , GLY D:487 , GLN D:488 , CYS D:516 , ZN D:802 , U E:12 , A E:15 , C F:10 , C F:11binding site for Di-nucleotide 8AZ E 13 and G E 14

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5ED2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5ED2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5ED2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5ED2)

(-) Exons   (0, 0)

(no "Exon" information available for 5ED2)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.....hhhhh...eeeeeee...hhh.eeeeeeee.eee.hhhhh........eeehhhhhhhhhhhhhhhhhhhhh....hhhhh.eee.....eee....eeeeee..................................eeee......ee........hhhhhhh....eeehhhhhhhhhhhhh.hhhhhh.......eeeeee....hhhhhhhhhhhhhh..............eee...............eeeeee......eeee..............hhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ed2 A 316 QLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGQGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 700
                                   325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695     


Chain B from PDB  Type:RNA  Length:23
                                                       
                 5ed2 B   1 GCUCGCGAUGCUxGAGGGCUCUG  23
                                    10  |     20   
                                       13-8AZ      


Chain C from PDB  Type:RNA  Length:23
                                                       
                 5ed2 C   1 CAGAGCCCCCCAGCAUCGCGAGC  23
                                    10        20   


Chain D from PDB  Type:PROTEIN  Length:385
                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.....hhhhh...eeeeeee...hhh.eeeeeeee.....hhhhh..........hhhhhhhhhhhhhhhhhhhhhh.hhhhhh...eee.....eee....eeeeee..................................eeee......ee........hhhhhhh....eeehhhhhhhhhhhhh.hhhhhh.......eeeeee....hhhhhhhhhhhhhh..............eeee..............eeeeee......eeee..............hhhhhhhhhhhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ed2 D 316 QLHLPQVLADAVSRLVLGKFGDLTDNFSSPHARRKVLAGVVMTTGTDVKDAKVISVSTGTKCINGEYMSDRGLALNDCHAEIISRRSLLRFLYTQLELYLNNKDDQKRSIFQKSERGGFRLKENVQFHLYISTSPCGDARIFSPHEPILEEPADRHPNRKARGQLRTKIESGQGTIPVRSNASIQTWDGVLQGERLLTMSCSDKIARWNVVGIQGSLLSIFVEPIYFSSIILGSLYHGDHLSRAMYQRISNIEDLPPLYTLNKPLLSGISNAEARQPGKAPNFSVNWTVGDSAIEVINATTGKDELGRASRLCKHALYCRWMRVHGKVPSHLLRSKITKPNVYHESKLAAKEYQAAKARLFTAFIKAGLGAWVEKPTEQDQFSLT 700
                                   325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695     


Chain E from PDB  Type:RNA  Length:23
                                                       
                 5ed2 E   1 GCUCGCGAUGCUxGAGGGCUCUG  23
                                    10  |     20   
                                       13-8AZ      


Chain F from PDB  Type:RNA  Length:23
                                                       
                 5ed2 F   1 CAGAGCCCCCCAGCAUCGCGAGC  23
                                    10        20
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5ED2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5ED2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5ED2)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    8AZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    IHP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5ed2)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5ed2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  RED1_HUMAN | P78563
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.5.4.37
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  RED1_HUMAN | P78563
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RED1_HUMAN | P78563: 1zy7 5ed1 5hp2 5hp3

(-) Related Entries Specified in the PDB File

5ed1